ArticleEcology and evolution2021
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
Article in Ecology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Making eDNA more digestible: A pizza analogy for understanding false negatives and occupancy modeling.Bioscience · 2026Review
- eDNA surveys substantially expand known geographic and ecological niche boundaries of marine fishes.PLoS biology · 2025Article
- Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed.Molecular ecology resources · 2025Article
- DNA State Influences the Uptake and Persistence of Environmental DNA by Marine Sponge Natural Samplers.Ecology and evolution · 2025Article
- An optimized eDNA protocol for fish tracking in estuarine environments.Scientific reports · 2025Article
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- Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes.Oecologia · 2023Article
- Evaluating the sampling effort for the metabarcoding-based detection of fish environmental DNA in the open ocean.Ecology and evolution · 2023Article
- Extracting abundance information from DNA-based data.Molecular ecology resources · 2023Review
- Environmental DNA persistence and fish detection in captive sponges.Molecular ecology resources · 2022Article
- Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem.Ecology and evolution · 2022Article
- Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring.Zoological research · 2022Article
- How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?Ecology and evolution · 2021Article
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Authors and funding
25 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
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